Remove extra materials output by serial geometry objects

gprMax/geometry_outputs.py

@@ -411,45 +411,45 @@ class GeometryObjects:
             pbar: Progress bar class instance.
         """
 
+        ID = G.ID[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
+
+        # Get materials present in subset of ID array
+        material_ids, inverse_map = np.unique(ID, return_inverse=True)
+
+        # Create map from material ID to 0 - number of materials
+        materials_map = {material_id: index for index, material_id in enumerate(material_ids)}
+
+        # Remap ID array to the reduced list of materials
+        ID = np.array([materials_map[id] for id in material_ids])[inverse_map].reshape(ID.shape)
+
+        data = G.solid[self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1].astype(
+            "int16"
+        )
+        map_materials = np.vectorize(lambda id: materials_map[id])
+        data = map_materials(data)
+
+        rigidE = G.rigidE[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
+        rigidH = G.rigidH[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
+
         with h5py.File(self.filename_hdf5, "w") as fdata:
             fdata.attrs["gprMax"] = __version__
             fdata.attrs["Title"] = title
             fdata.attrs["dx_dy_dz"] = (G.dx, G.dy, G.dz)
 
-            # Get minimum and maximum integers of materials in geometry objects volume
-            minmat = np.amin(
-                G.ID[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
-            )
-            maxmat = np.amax(
-                G.ID[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
-            )
-            fdata["/data"] = (
-                G.solid[self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1].astype(
-                    "int16"
-                )
-                - minmat
-            )
+            fdata["/data"] = data
             pbar.update(self.solidsize)
-            fdata["/rigidE"] = G.rigidE[
-                :, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1
-            ]
-            fdata["/rigidH"] = G.rigidH[
-                :, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1
-            ]
+
+            fdata["/rigidE"] = rigidE
+            fdata["/rigidH"] = rigidH
             pbar.update(self.rigidsize)
-            fdata["/ID"] = (
-                G.ID[:, self.xs : self.xf + 1, self.ys : self.yf + 1, self.zs : self.zf + 1]
-                - minmat
-            )
+
+            fdata["/ID"] = ID
             pbar.update(self.IDsize)
 
         # Write materials list to a text file
-        # This includes all materials in range whether used in volume or not
         with open(self.filename_materials, "w") as fmaterials:
-            for numID in range(minmat, maxmat + 1):
-                for material in G.materials:
-                    if material.numID == numID:
-                        self.output_material(material, fmaterials)
+            for numID in material_ids:
+                self.output_material(G.materials[numID], fmaterials)
 
     def output_material(self, material: Material, file: TextIOWrapper):
         file.write(